diff IDEvaluator.xml @ 0:3d84209d3178 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IDEvaluator.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,54 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="IDEvaluator" name="IDEvaluator" version="1.12.0">
+  <description>Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value.</description>
+  <macros>
+    <token name="@EXECUTABLE@">IDEvaluator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>IDEvaluator
+
+-in ${param_in}
+-out ${param_out}
+-out_type ${param_out_type}
+-out_csv ${param_out_csv}
+-q_min ${param_q_min}
+-q_max ${param_q_max}
+-threads \${GALAXY_SLOTS:-24} 
+${param_use_all_hits}
+-algorithm:image:height ${param_height}
+-algorithm:image:width ${param_width}
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="idXML" optional="True" size="20" label="Input file(s)" help="(-in)"/>
+    <param name="param_out_type" type="select" optional="True" label="The image format. Set this if you want to force a format not reflected by the 'out' filename." help="(-out_type)">
+      <option value="png">png</option>
+      <option value="jpg">jpg</option>
+      <option value="svg">svg</option>
+    </param>
+    <param name="param_q_min" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimal q-value in plot." help="(-q_min)"/>
+    <param name="param_q_max" type="float" min="0.0" max="1.0" optional="True" value="0.4" label="Maximal q-value in plot." help="(-q_max)"/>
+    <param name="param_use_all_hits" type="boolean" truevalue="-algorithm:fdr:use_all_hits true" falsevalue="-algorithm:fdr:use_all_hits false" checked="false" optional="True" label="If 'true' not only the first hit, but all are used (peptides only)" help="(-use_all_hits)"/>
+    <param name="param_height" type="integer" value="800" label="Height of raster images (e.g., PNG)." help="(-height)"/>
+    <param name="param_width" type="integer" value="1024" label="Width of raster images (e.g., PNG)." help="(-width)"/>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="Output file (if given, no GUI will be displayed)" format="svg">
+      <change_format>
+        <when input="param_out_type" value="png" format="png"/>
+        <when input="param_out_type" value="jpg" format="jpg"/>
+      </change_format>
+    </data>
+    <data name="param_out_csv" label="Optional output of points as table for manual post-processing." format="tabular"/>
+  </outputs>
+  <help>**What it does**
+
+Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDEvaluator.html
+
+@REFERENCES@
+</help>
+</tool>